My battery suddenly fully depletes when below a certain (and not always the same) charge threshold and afterwards recharging through the micro USB plug is no longer possible (the circular indicator at the bottom of the screen blinks, but the battery does not get charged). The battery has to be taken out and has to be charged through an external charger.

I have already changed battery and battery connector but the problem remains.

Is this a known issue? And would it be rather motherboard or OS (Ubuntu Touch OTA-14) related?

I realize this is a Flyme-oriented forum, but I have not a lot of other channels to turn to. So, thanks for any advice!

First of all welcome. Second, we are a Meizu, not a Flyme fan community ;)
Nonetheless, here some things you maybe want to check as well:

Is the wall plug okay?
My Pro 5 once stopped charging as the charger broke. I paniced of course, thinking that my phone was broken. So maybe go and try a different one.

In case you are sure that its not the chargers fold, you should take a look at the mainboard.
You can get a replacement on AliExpress in most of the cases, but as you own an Ubuntu Edition MX4, it might be difficuilt to get one.

The wall plug is definitely OK. The phone actually charges fine -using the same wall plug and phone cable- when the battery is not entirely depleted. Once it gets depleted, the battery has to be taken out and charged externally.

The other option I have is to try to keep the battery charged, and to buy an external charging device to use in case I inadvertently fully deplete the battery. Any reference to such an external charging device I could use on the BT40 battery?

Reading the thread you have pointed to, I see that not many people have been able to reproduce the flashing instructions and the thread contains many additional and sometimes conflicting instructions. So, without a clearer guide I’m a bit hesistating to buy a new Flyme OS containing motherboard.